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blastn

List of commands for blastn:

  • blastn:tldr:036f3 blastn: Search nucleotide databases using a nucleotide query, 16 threads (CPUs) to use in the BLAST search, with a maximum number of 10 aligned sequences to keep.
    $ blastn -query ${query-fa} -db ${path-to-blast_db} -num_threads ${16} -max_target_seqs ${10}
    try on your machine
    explain this command
  • blastn:tldr:1dc78 blastn: Align two or more sequences using megablast (default), with the e-value threshold of 1e-9, pairwise output format (default).
    $ blastn -query ${query-fa} -subject ${subject-fa} -evalue ${1e-9}
    try on your machine
    explain this command
  • blastn:tldr:c0c63 blastn: Display help (use `-help` for detailed help).
    $ blastn -h
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  • blastn:tldr:c3f99 blastn: Search the remote non-redundant nucleotide database using a nucleotide query.
    $ blastn -query ${query-fa} -db ${nt} -remote
    try on your machine
    explain this command
  • blastn:tldr:cae83 blastn: Align two or more sequences, custom tabular output format, output to file.
    $ blastn -query ${query-fa} -subject ${subject-fa} -outfmt ${'6 qseqid qlen qstart qend sseqid slen sstart send bitscore evalue pident'} -out ${output-tsv}
    try on your machine
    explain this command
  • blastn:tldr:e9af8 blastn: Align two or more sequences using blastn.
    $ blastn -task blastn -query ${query-fa} -subject ${subject-fa}
    try on your machine
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